|
| Status |
Public on Jul 31, 2013 |
| Title |
Peripheral blood mononuclear cells of 195-Cy3 post-treatment dasatinib responder patient |
| Sample type |
RNA |
| |
|
| Source name |
Total RNA from peripheral blood mononuclear cells of post-treatment labeled with Cyanine-3
|
| Organism |
Homo sapiens |
| Characteristics |
dasatinib treatment: Post-treatment
drug response: non-responder
cell type: peripheral blood mononuclear cells
gender: female
age (yrs) at dasatinib start: 63
treatments prior to dasatinib: HU, IFN, araC, IM
mutations detected in the bcr/abl kinase domain before dasatinib treatment: not detected
ph+ metaphases before dasatinib treatment (%): 90
additional cytogenetic abnormalities after dasatinib treatment: not detected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent (Invitrogen), treated with RNase-free DNase I and purified using the RNeasy kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Agilent Two-Color Microarray-Based Gene Expression Analysis protocol: Starting with 200 ng of total RNA, we performed cDNA synthesis and generated fluorescent labeled cRNA targets using Agilent Low RNA Input Fluorescent Linear Amplification Kit and oligo-dT-T7 promoter primer. Each patient sample was separately labeled with Cy3 and Cy5 to perform a dye swap technical replicate.
|
| |
|
| Hybridization protocol |
825ng of each Cy3 and Cy5 labeled cRNA was hybridized using Agilent Gene Expression Hybridization Kit.
|
| Scan protocol |
Slides were scanned immediately after washing on the Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA).
|
| Description |
Raw data file:
251559510046_2007-07-20_570_566_GE2-v5_95_Feb07_1_4.txt
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software v.9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities (Processed Signal feature column from raw data archive). Gene probes were considered in the analysis only when they were detected in 80% of the arrays. Data were normalized among the samples by quantile method.
The normalized processed signal intensities for each channel on each (dual-channel) array are the normalized/processed data that form the basis of the conclusions of study.
NR.Y.T3.195Cy3_post
|
| |
|
| Submission date |
Oct 27, 2011 |
| Last update date |
Jul 31, 2013 |
| Contact name |
Angela A. Fachel |
| E-mail(s) |
[email protected]
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
1300 York Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL9193 |
| Series (2) |
| GSE33288 |
Noncoding RNA expression profile of dasatinib-treated chronic myeloid leukemia patients with resistance to imatinib |
| GSE33290 |
Gene expression signatures of dasatinib-treated chronic myeloid leukemia patients with resistance to imatinib |
|
